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comparison deepvariant.xml @ 1:97cc305f6afe draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit ce3024e2098c50a93ea8a7fc120a40a570fd0c53"
author iuc
date Fri, 01 Oct 2021 07:46:04 +0000
parents 2036bbf304d6
children 1071eaa424a2
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0:2036bbf304d6 1:97cc305f6afe
29 #if $regions_conditional.regions_option == 'region' 29 #if $regions_conditional.regions_option == 'region'
30 --regions $regions_conditional.region_literal 30 --regions $regions_conditional.region_literal
31 #else if $regions_conditional.regions_option == 'bed' 31 #else if $regions_conditional.regions_option == 'bed'
32 --regions region.bed 32 --regions region.bed
33 #end if 33 #end if
34 --call_variants_extra_args="use_openvino=true" ## Setting this will use OpenVINO on Intel CPUs, which empirically reduces call_variants runtime by 15%-25%. 34 ##--call_variants_extra_args="use_openvino=true" ## Setting this will use OpenVINO on Intel CPUs, which empirically reduces call_variants runtime by 15%-25%.
35 --num_shards=\${GALAXY_SLOTS:-2} 35 --num_shards=\${GALAXY_SLOTS:-2}
36 && gunzip './output.vcf.gz' 36 && gunzip './output.vcf.gz'
37 #if $output_gvcf 37 #if $output_gvcf
38 && gunzip './output.g.vcf.gz' 38 && gunzip './output.g.vcf.gz'
39 #end if 39 #end if
54 </when> 54 </when>
55 <when value="history"> 55 <when value="history">
56 <param name="history_item" type="data" format="fasta" label="Reference genome" help="A reference genome in FASTA format" /> 56 <param name="history_item" type="data" format="fasta" label="Reference genome" help="A reference genome in FASTA format" />
57 </when> 57 </when>
58 </conditional> 58 </conditional>
59 <param argument="--reads" type="data" format="BAM" label="BAM file" help="An aligned reads files for child and one or two parents in BAM format. The reads must be aligned to the reference genome" /> 59 <param argument="--reads" type="data" format="BAM" label="BAM file" help="An aligned reads file in BAM format. The reads must be aligned to the reference genome" />
60 <param argument="--model_type" type="select" label="Model type" help="Type of model to use for variant calling"> 60 <param argument="--model_type" type="select" label="Model type" help="Type of model to use for variant calling">
61 <option value="WGS">WGS: Illumina whole genome sequencing</option> 61 <option value="WGS">WGS: Illumina whole genome sequencing</option>
62 <option value="WES">WES: Illumina whole exome sequencing</option> 62 <option value="WES">WES: Illumina whole exome sequencing</option>
63 <option value="PACBIO">PacBio HiFi</option> 63 <option value="PACBIO">PacBio HiFi</option>
64 <option value="HYBRID_PACBIO_ILLUMINA">Hybrid PacBio HiFi-Illumina</option> 64 <option value="HYBRID_PACBIO_ILLUMINA">Hybrid PacBio HiFi-Illumina</option>